Implement rolling Gini graph; bump version to 0.16.2

src/seismicrna/core/mu/__init__.py

@@ -3,6 +3,7 @@
 from .frame import *
 from .nan import *
 from .scale import *
+from .trends import *
 from .unbias import *
 
 ########################################################################

src/seismicrna/core/version.py

@@ -7,7 +7,7 @@
 
 logger = getLogger(__name__)
 
-__version__ = "0.16.1"
+__version__ = "0.16.2"
 
 
 def parse_version(version: str = __version__):

src/seismicrna/graph/aucroll.py

@@ -11,7 +11,7 @@
                         StructOneTableRunner,
                         StructOneTableWriter)
 from .roc import PROFILE_NAME, rename_columns
-from .roll import RollingGraph
+from .roll import RollingGraph, RollingRunner
 from .trace import iter_rolling_auc_traces
 from ..core.arg import opt_window, opt_winmin
 
@@ -70,11 +70,7 @@ def get_graph(self, rels_group: str, **kwargs):
         return RollingAUCGraph(table=self.table, rel=rels_group, **kwargs)
 
 
-class RollingAUCRunner(StructOneTableRunner, PosGraphRunner):
-
-    @classmethod
-    def var_params(cls):
-        return super().var_params() + [opt_window, opt_winmin]
+class RollingAUCRunner(RollingRunner, StructOneTableRunner, PosGraphRunner):
 
     @classmethod
     def get_writer_type(cls):

src/seismicrna/graph/corroll.py

@@ -6,10 +6,10 @@
 from plotly import graph_objects as go
 
 from .base import PosGraphWriter, PosGraphRunner
-from .roll import RollingGraph
-from .twotable import TwoTableMergedGraph, TwoTableRunner, TwoTableWriter
+from .roll import RollingGraph, RollingRunner
 from .trace import iter_seq_line_traces
-from ..core.arg import opt_metric, opt_window, opt_winmin
+from .twotable import TwoTableMergedGraph, TwoTableRunner, TwoTableWriter
+from ..core.arg import opt_metric
 from ..core.mu import compare_windows, get_comp_name
 
 logger = getLogger(__name__)
@@ -66,11 +66,11 @@ def get_graph_type(cls):
         return RollingCorrelationGraph
 
 
-class RollingCorrelationRunner(TwoTableRunner, PosGraphRunner):
+class RollingCorrelationRunner(RollingRunner, TwoTableRunner, PosGraphRunner):
 
     @classmethod
     def var_params(cls):
-        return super().var_params() + [opt_metric, opt_window, opt_winmin]
+        return super().var_params() + [opt_metric]
 
     @classmethod
     def get_writer_type(cls):

src/seismicrna/graph/giniroll.py

@@ -0,0 +1,104 @@
+import os
+from functools import cached_property
+from logging import getLogger
+
+import pandas as pd
+from click import command
+from plotly import graph_objects as go
+
+from .base import PosGraphWriter, PosGraphRunner
+from .onetable import OneTableGraph, OneTableRunner, OneTableWriter
+from .rel import OneRelGraph
+from .roll import RollingGraph, RollingRunner
+from .trace import iter_rolling_gini_traces
+from ..core.header import format_clust_name
+from ..core.mu import calc_gini
+from ..core.seq import iter_windows
+
+logger = getLogger(__name__)
+
+COMMAND = __name__.split(os.path.extsep)[-1]
+
+
+class RollingGiniGraph(OneTableGraph, OneRelGraph, RollingGraph):
+
+    @classmethod
+    def graph_kind(cls):
+        return COMMAND
+
+    @classmethod
+    def what(cls):
+        return "Rolling Gini coefficient"
+
+    @property
+    def y_title(self):
+        return "Gini"
+
+    @cached_property
+    def data(self):
+        data = self._fetch_data(self.table,
+                                order=self.order,
+                                clust=self.clust)
+        gini = pd.DataFrame(index=data.index, dtype=float)
+        for cluster, cluster_data in data.items():
+            cluster_gini = pd.Series(index=gini.index, dtype=float)
+            for center, (window,) in iter_windows(cluster_data,
+                                                  size=self._size,
+                                                  min_count=self._min_count):
+                cluster_gini.loc[center] = calc_gini(window)
+            if isinstance(cluster, tuple):
+                _, order, clust = cluster
+                label = format_clust_name(order, clust)
+            else:
+                label = cluster
+            gini[label] = cluster_gini
+        return gini
+
+    def get_traces(self):
+        for row, trace in enumerate(iter_rolling_gini_traces(self.data),
+                                    start=1):
+            yield (row, 1), trace
+
+    def _figure_layout(self, fig: go.Figure):
+        super()._figure_layout(fig)
+        fig.update_yaxes(gridcolor="#d0d0d0")
+
+
+class RollingGiniWriter(OneTableWriter, PosGraphWriter):
+
+    def get_graph(self, rels_group: str, **kwargs):
+        return RollingGiniGraph(table=self.table, rel=rels_group, **kwargs)
+
+
+class RollingGiniRunner(RollingRunner, OneTableRunner, PosGraphRunner):
+
+    @classmethod
+    def get_writer_type(cls):
+        return RollingGiniWriter
+
+
+@command(COMMAND, params=RollingGiniRunner.params())
+def cli(*args, **kwargs):
+    """ Rolling Gini coefficient. """
+    return RollingGiniRunner.run(*args, **kwargs)
+
+########################################################################
+#                                                                      #
+# © Copyright 2024, the Rouskin Lab.                                   #
+#                                                                      #
+# This file is part of SEISMIC-RNA.                                    #
+#                                                                      #
+# SEISMIC-RNA is free software; you can redistribute it and/or modify  #
+# it under the terms of the GNU General Public License as published by #
+# the Free Software Foundation; either version 3 of the License, or    #
+# (at your option) any later version.                                  #
+#                                                                      #
+# SEISMIC-RNA is distributed in the hope that it will be useful, but   #
+# WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANT- #
+# ABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General     #
+# Public License for more details.                                     #
+#                                                                      #
+# You should have received a copy of the GNU General Public License    #
+# along with SEISMIC-RNA; if not, see <https://www.gnu.org/licenses>.  #
+#                                                                      #
+########################################################################

src/seismicrna/graph/main.py

@@ -3,6 +3,7 @@
 from . import (aucroll,
                corroll,
                delprof,
+               giniroll,
                histpos,
                histread,
                profile,
@@ -21,6 +22,7 @@ def cli():
 for module in (aucroll,
                corroll,
                delprof,
+               giniroll,
                histpos,
                histread,
                profile,

src/seismicrna/graph/roll.py

@@ -1,7 +1,8 @@
 from abc import ABC
 from functools import cached_property
 
-from .base import GraphBase
+from .base import GraphBase, GraphRunner
+from ..core.arg import opt_window, opt_winmin
 from ..core.seq import POS_NAME
 
 
@@ -28,6 +29,13 @@ def predicate(self):
              "-".join(map(str, [self._size, self._min_count]))]
         )
 
+
+class RollingRunner(GraphRunner, ABC):
+
+    @classmethod
+    def var_params(cls):
+        return super().var_params() + [opt_window, opt_winmin]
+
 ########################################################################
 #                                                                      #
 # © Copyright 2024, the Rouskin Lab.                                   #

src/seismicrna/graph/trace.py

@@ -175,6 +175,16 @@ def iter_rolling_auc_traces(aucs: pd.DataFrame, profile: str):
         yield get_rolling_auc_trace(auc, profile, str(struct))
 
 
+def get_rolling_gini_trace(gini: pd.Series, cluster: str):
+    return go.Scatter(x=gini.index.get_level_values(POS_NAME),
+                      y=gini,
+                      name=cluster)
+
+
+def iter_rolling_gini_traces(ginis: pd.DataFrame):
+    for cluster, gini in ginis.items():
+        yield get_rolling_gini_trace(gini, str(cluster))
+
 ########################################################################
 #                                                                      #
 # © Copyright 2024, the Rouskin Lab.                                   #